Yes, i kept the copies of the saves, for the momento only the first shadow pokemon battle.
I upload the saves.
I have made a little program in C# where i decrypted the file and extracted the save file data using the algotirhm from the program PkmGCSaveEditor (I'm a C# developer), i include also dat files with de savedata already decrypted. The dat files have only the data of the last saveslot from every save, Pokemon Colloseum save files have 3 copies of the save inside the file in case one or two is corrupt.
I analyzed the changed data between saves
Starting in position 9ABF there is the data of the Normal E-Reader Trainers already defeated. 20 ocurrences of 16 bytes each one, one from every trainer. Probably it can be more trainers stored because you can fight a promotional trainer with a promotional e-reader card that is not part of the 20 normal cards. The 16 bytes structure is 10 bytes for the trainer name, then 00 01 00 00 01, the secon trainer have in this part 00 01 00 00 02 and so on. The second number is clearly the number of the trainer to show in order, from 1 to 20, the first 01 it should mean is has been defeated in easy mode, i suppose the other zeros will change when is defeated in other difficulty modes.
The data of the four special trainer is stored starting 9A59, that means special trainers are stored before normal trainers, this time only 14 bytes per trainer. There is clearly space for 7 special trainers, the first 4 are the ones defeated after every 5 normal e-reader trainers, the other space maybe is used with the special trainers onlucked with the promotional e-reader cards, there was only two cards edited, only one is dumped in raw format. I dont know, i have to check the save files after defeating the promotional a-reader trainer, but i wont do that after unlocking the 3 shadow pokemons.
Every special trainer have 00 01 00 00 after his name, that means there is not saved the trainer number like the normal trainers, only the bytes for defeated in every mode (I only tested easy mode, but there is 4 possible modes, easy, normal, hard and endless).
Ok, now the fun part, shadow trainer. In the save after defeating trainer 20 and special trainer 4 it changes a lot, not just the names of the last two trainers like the others. I have one save with 19 trainers and 3 special trainers and another after defeating 20 and 4 and it not only changes the trainers list. From DA24 to DC06 all this is filled with data that in the save before unlocked the shadow trainer was everithing zero's. I think that is all the information of the Shadow Trainer, that means none of the e-reader trainers data is stored in the game, is everithing readed from the card, not only the normal trainers, but also the fight with special trainers and shadow trainers.
In 1BB0C it change also from 0s to 30 DC 30 C7 30 B9 00 00 00 00 00 00 1E 00. It could be the data of the shadow pokemon from the shadow list, i'm not sure yet. I dont know what is the data stored in this area, it seems a list of something.
After chatching the shadow pokemon there is more changes, i ignore those that happens around the party pokemon data and the bank data of course. It chenges in the position 9AB9 from 00 to 01. This are is between the special trainers and the normal e-reader trainers. DA24, in the data just before all the shadow trianer data, has changed from 0 to 1. 1B01F change from 30 to 31, in decimal from 48 to 49, just the number of shadow pokemon captured. In 1B353 there is 07 C6 90 38 09 00 00 00 80, before it was 0's
1BDC5 changed from 0 to 1
1BB20 changed from FF FF 00 32 to 00 30 00 46. Is in the same part of the list mentioned with the changes in 1BB0C. I could be the shadow pokemon list.
Ok, the next part will be trying to inject this data to a save without doing nothing in the e-reader room to make the trainer appears. The data from DA24 to DC06 is the first we should try. That should make the trainer appears.
And last, a link with the save files
https://mega.nz/#!aZtjWS5K!-ofYUkW2_5jpf9PGT3odpEuO49ZTNOwlZimjFY7Df7o